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Cryo-EM structure of amprolium-bound human SLC19A3 in inward-open state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Refinement RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.764 r_dihedral_angle_6_deg 16.529 r_dihedral_angle_1_deg 4.355 r_angle_refined_deg 1.36 r_angle_other_deg 0.602 r_dihedral_angle_2_deg 0.467 r_symmetry_nbd_other 0.248 r_nbd_refined 0.247 r_nbtor_refined 0.215 r_xyhbond_nbd_refined 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.764 r_dihedral_angle_6_deg 16.529 r_dihedral_angle_1_deg 4.355 r_angle_refined_deg 1.36 r_angle_other_deg 0.602 r_dihedral_angle_2_deg 0.467 r_symmetry_nbd_other 0.248 r_nbd_refined 0.247 r_nbtor_refined 0.215 r_xyhbond_nbd_refined 0.16 r_symmetry_nbtor_other 0.079 r_symmetry_xyhbond_nbd_other 0.067 r_chiral_restr 0.057 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_lrange_it r_lrange_other
Sample SLC19A3:Nb3.7:amprolium Sample Components SLC19A3 Nb3.7
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE-PROPANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 437310 Reported Resolution (Å) 3.75 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 Refinement Space REAL Refinement Protocol AB INITIO MODEL Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 46
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 1600 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification 105000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC MODEL FITTING ISOLDE MODEL REFINEMENT PHENIX INITIAL EULER ASSIGNMENT cryoSPARC FINAL EULER ASSIGNMENT cryoSPARC CLASSIFICATION cryoSPARC RECONSTRUCTION cryoSPARC
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION